Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences
Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. Discussion The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.
Sjakste et al. (2020) Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences. PeerJ 8:e8569 https://doi.org/10.7717/peerj.8569
Nomograms predict survival outcome of Klatskin tumors patients
Objective Klatskin tumors are rare, malignant tumors of the biliary system with a poor prognosis for patient survival. The current understanding of these tumors is limited to a small number of case reports or case series; therefore, we examined prognostic factors of this disease. Methods A population cohort study was conducted in patients selected from the Surveillance, Epidemiology, and End Results (SEER) database with a Klatskin tumor that was histologically diagnosed between 2004 to 2014. Propensity-matching (PSM) analysis was performed to determine the overall survival (OS) among those with a Klatskin tumor (KCC), intrahepatic cholangiocarcinoma (ICCA), or hepatocellular carcinoma (HCC). The nomogram was based on 317 eligible Klatskin tumor patients and its predictive accuracy and discriminatory ability were determined using the concordance index (C-index). Results Kaplan-Meier analysis showed that patients with Klatskin tumors had significantly worse overall survival rates (1-year OS = 26.2%, 2-year OS = 10.7%, 3-year OS = 3.4%) than those with intrahepatic cholangiocarcinoma (1-year OS = 62.2%, 2-year OS = 36.4%, 3-year OS = 19.1%, p < 0.001) or hepatocellular carcinoma (1-year OS = 72.4% , 2-year OS = 48.5%, 3-year OS = 36.2%, p < 0.001). A poor prognosis was also significantly associated with older age, higher grade, SEER historic stage, and lymph node metastasis. Local destruction of the tumor (HR = 0.635, 95% CI [0.421–0.956], p = 0.03) and surgery (HR = 0.434, 95% [CI 0.328–0.574], p < 0.001) were independent protective factors. Multivariate Cox analysis showed that older age, SEER historic stage, and lymph node metastases (HR = 1.468, 95% CI [1.008–2.139], p = 0.046) were independent prognostic factors of poor survival rates in Klatskin tumor patients, while cancer-directed surgery was an independent protective factor (HR = 0.555, 95% CI [0.316–0.977], p = 0.041). The prognostic and protective factors were included in the nomogram (C-index for survival = 0.651; 95% CI [0.607–0.695]). Conclusions The Klatskin tumor group had poorer rates of OS and cancer-specific survival than the ICCA and HCC groups. Early detection and diagnosis were associated with a higher rate of OS in Klatskin tumor patients.
Qi et al. (2020) Nomograms predict survival outcome of Klatskin tumors patients. PeerJ 8:e8570 https://doi.org/10.7717/peerj.8570
No island-effect on glucocorticoid levels for a rodent from a near-shore archipelago
Island rodents are often larger and live at higher population densities than their mainland counterparts, characteristics that have been referred to as “island syndrome”. Island syndrome has been well studied, but few studies have tested for island-mainland differences in stress physiology. We evaluated island syndrome within the context of stress physiology of white-footed mice (Peromyscus leucopus) captured from 11 islands and five mainland sites in Thousand Islands National Park, Ontario, Canada. Stress physiology was evaluated by quantifying corticosterone (a stress biomarker), the primary glucocorticoid in mice, from hair and its related metabolites from fecal samples. White-footed mice captured in this near-shore archipelago did not display characteristics of island syndrome, nor differences in levels of hair corticosterone or fecal corticosterone metabolites compared with mainland mice. We suggest that island white-footed mice experience similar degrees of stress in the Thousand Islands compared with the mainland. Although we did not find evidence of island syndrome or differences in glucocorticoid levels, we identified relationships between internal (sex, body mass) and external (season) factors and our hormonal indices of stress in white-footed mice.
Stewart et al. (2020) No island-effect on glucocorticoid levels for a rodent from a near-shore archipelago. PeerJ 8:e8590 https://doi.org/10.7717/peerj.8590
Effectiveness of slightly acidic electrolyzed water on bacteria reduction: in vitro and spray evaluation
Bacterial inactivation is a crucial aspect of sanitation and hygiene. The effectiveness of slightly acidic electrolyzed water (SAEW) for reduction or removal of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus epidermidis was evaluated. The bactericidal activity of SAEW and sodium hypochlorite (NaOCl) against E. coli and P. aeruginosa were compared through in vitro experiments. The effectiveness of SAEW spray was tested against S. epidermidis. Results showed that SAEW had a more powerful bactericidal activity than NaOCl at the same available chlorine concentrations. For E. coli, SAEW decreased the bacterial counts from 8.4 log10 CFU/mL to less than 3.9 log10 CFU/mL; NaOCl with the same available chlorine of 0.5 mg/L, caused a decrease from 8.4 log10 CFU/mL to 7.1 log10 CFU/mL. For P. aeruginosa, SAEW caused bacterial counts to decrease from 8.5 log10 CFU/mL to less than 4.1 log10 CFU/mL against 8.5 log10 CFU/mL to 6.2 log10 CFU/mL for NaOCl with the same available chlorine of 0.5 mg/L. Spray experiments showed that 10 mg/L of SAEW spray decreased the bacterial counts of S. epidermidis from 3.7 log10 CFU/m3 to 2.8 log10 CFU/m3, with 20 mg/L causing a reduction from 3.8 log10 CFU/m3 to 0 CFU/m3. The overall findings of this study indicate that SAEW may be a promising disinfectant agent either as a solution or spray.
Naka et al. (2020) Effectiveness of slightly acidic electrolyzed water on bacteria reduction: in vitro and spray evaluation. PeerJ 8:e8593 https://doi.org/10.7717/peerj.8593
Fasciola gigantica, F. hepatica and Fasciola intermediate forms: geometric morphometrics and an artificial neural network to help morphological identification
Background Fasciola hepatica and F. gigantica cause fascioliasis in both humans and livestock. Some adult specimens of Fasciola sp. referred to as “intermediate forms” based on their genetic traits, are also frequently reported. Simple morphological criteria are unreliable for their specific identification. In previous studies, promising phenotypic identification scores were obtained using morphometrics based on linear measurements (distances, angles, curves) between anatomical features. Such an approach is commonly termed “traditional” morphometrics, as opposed to “modern” morphometrics, which is based on the coordinates of anatomical points. Methods Here, we explored the possible improvements that modern methods of morphometrics, including landmark-based and outline-based approaches, could bring to solving the problem of the non-molecular identification of these parasites. F. gigantica and Fasciola intermediate forms suitable for morphometric characterization were selected from Thai strains following their molecular identification. Specimens of F. hepatica were obtained from the Liverpool School of Tropical Medicine (UK). Using these three taxa, we tested the taxonomic signal embedded in traditional linear measurements versus the coordinates of anatomical points (landmark- and outline-based approaches). Various statistical techniques of validated reclassification were used, based on either the shortest Mahalanobis distance, the maximum likelihood, or the artificial neural network method. Results Our results revealed that both traditional and modern morphometric approaches can help in the morphological identification of Fasciola sp. We showed that the accuracy of the traditional approach could be improved by selecting a subset of characters among the most contributive ones. The influence of size on discrimination by shape was much more important in traditional than in modern analyses. In our study, the modern approach provided different results according to the type of data: satisfactory when using pseudolandmarks (outlines), less satisfactory when using landmarks. The different reclassification methods provided approximately similar scores, with a special mention to the neural network, which allowed improvements in accuracy by combining data from both morphometric approaches. Conclusion We conclude that morphometrics, whether traditional or modern, represent a valuable tool to assist in Fasciola species recognition. The general level of accuracy is comparable among the various methods, but their demands on skills and time differ. Based on the outline method, our study could provide the first description of the shape differences between species, highlighting the more globular contours of the intermediate forms.
Sumruayphol et al. (2020) Fasciola gigantica, F. hepatica and Fasciola intermediate forms: geometric morphometrics and an artificial neural network to help morphological identification. PeerJ 8:e8597 https://doi.org/10.7717/peerj.8597
Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample
Background Injuries are among the most important threats to adolescent health, making examination of the patterns and risk factors a critical area of research. There exists a paucity of information on the health and injury experience of school-attending adolescents in Greenland. Consenting Greenlandic schoolchildren (n = 2,254) aged 9–19 years were included in the Health Behavior in School-Aged Children study 2005/2006. The aim of this study was to examine the socio-economic and behavioural correlates that were associated with injury occurrence among school-attending Greenlandic adolescents. Methods This study made use of two multinomial regression models to examine injury occurrence regarding potential influencing factors such as physical activity, risk behaviours, bullying and family socio-economic status (SES). Results Those self-reporting 1–2 injuries within the recall period were more likely to be male (OR = 1.70; CI [1.39–2.09]), involved in physical fighting (OR = 1.82; CI [1.33–2.47]), bullied (OR = 1.81; CI [1.47–2.24]) and participated in bullying others (OR = 1.53; CI [1.25–1.89]). Those reporting three or more injuries were again mostly male (OR = 2.13; CI [1.44–3.14]), involved in physical fighting at higher rates (OR = 4.47; CI [2.86–7.01]), bullied more often (OR = 2.43; CI [1.65–3.57]) and were more likely to bully others (OR = 1.67; CI [1.13–2.45]). Living without a mother proved to be significantly correlated with suffering 3 or more injuries during the recall period (OR = 1.63; CI [1.05–2.52]). The study results support the idea that factors that were found to be associated with injury occurrence, such as bullying and aggressive behaviour, should be taken into account when conducting future research on the nature of injuries among Greenlandic adolescents. More research on this topic is needed to identify factors that might modify the associations between injuries and adolescent behaviour and SES.
Jansen et al. (2020) Injuries among adolescents in Greenland: behavioural and socio-economic correlates among a nationally representative sample. PeerJ 8:e8605 https://doi.org/10.7717/peerj.8605
Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis
Background Juvenile dermatomyositis (JDM) is an immune-mediated disease characterized by chronic organ inflammation. The pathogenic mechanisms remain ill-defined. Methods Raw microarray data of JDM were obtained from the gene expression omnibus (GEO) database. Based on the GSE3307 dataset with 39 samples, weighted correlation network analysis (WGCNA) was performed to identify key modules associated with pathological state. Functional enrichment analyses were conducted to identify potential mechanisms. Based on the criteria of high connectivity and module membership, candidate hub genes were selected. A protein-protein interaction network was constructed to identify hub genes. Another dataset (GSE11971) was used for the validation of real hub genes. Finally, the real hub genes were used to screen out small-molecule compounds via the Connectivity map database. Results Three modules were considered as key modules for the pathological state of JDM. Functional enrichment analysis indicated that responses to interferon and metabolism were dysregulated. A total of 45 candidate hub genes were selected according to the pre-established criteria, and 20 genes could differentiate JDM from normal controls by validation of another external dataset (GSE11971). These real hub genes suggested the pivotal role of mitochondrial dysfunction and interferon signature in JDM. Furthermore, drug repositioning highlighted the importance of acacetin, helveticoside, lanatoside C, deferoxamine, LY-294002, tanespimycin and L01AD from downregulated genes with the potential to perturb the development of JDM, while betonicine, felodipine, valproic acid, trichostatin A and sirolimus from upregulated genes provided potentially therapeutic goals for JDM. Conclusions There are 20 real hub genes associated with the pathological state of JDM, suggesting the pivotal role of mitochondrial dysfunction and interferon signature in JDM. This analysis predicted several kinds of small-molecule compounds to treat JDM.
Zhong et al. (2020) Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis. PeerJ 8:e8611 https://doi.org/10.7717/peerj.8611
Association between 9-minute walk/run test and obesity among children and adolescents: evidence for criterion-referenced cut-points
Background Criterion-referenced cut-points for field-based aerobic fitness for children and adolescents are lacking. This study aimed to determine the associations between aerobic fitness and obesity to propose criterion-referenced cut-points for boys and girls (6–17 years). Methods A total of 61,465 children and adolescents aged 11.2 ± 2.0 years were recruited from 27 sites (all 26 states and Federal District) across Brazil. Aerobic fitness was assessed using 9-min walk/run test reported as distance attained during the test. Body mass index was calculated from measured height and weight and was used to identify obesity. Results The distance covered in the 9-min walk/run test (area under curve > 0.65) had satisfactory predictive ability for obesity. Sensitivity and specificity were moderate (>60%) to strong (>70%) for all age- and sex-specific cut-points. For boys, the optimal physical performance cut-points were, approximately, 1,200 m from 6 to 8 years, 1,300 m from 9 to 11 years, 1,380 m from 12 to 14 years, 1,520 m from 15 to 17 years. For girls, the best cut-points were, approximately, 1,070 m from 6 to 8 years, 1,160 m from 9 to 11 years and 1,200 m from 12 to 17 years. Conclusions The 9-min walk/run test had satisfactory predictive ability for obesity in children and adolescents. The physical fitness cut-points proposed in the present study varied according to age and sex and could be useful and practical tools to identify low levels of physical fitness in children and adolescents in Brazil.
Silva et al. (2020) Association between 9-minute walk/run test and obesity among children and adolescents: evidence for criterion-referenced cut-points. PeerJ 8:e8651 https://doi.org/10.7717/peerj.8651
Molecular phylogeny and intraspecific differentiation of the Trapelus agilis species complex in Iran (Squamata: Agamidae) inferred from mitochondrial DNA sequences
Background Trapelus agilis consists of different morphotypes with restricted distributions in the Iranian Plateau. The phylogeny of the species complex has not been resolved so far, but recently Trapelus sanguinolentus were elevated from this complex into a full species. Other populations of the species complex need to be evaluated taxonomically. Methods In the present study, several populations of this species complex along with specimens of its closely related taxa in Iran, T. sanguinolentus, T. ruderatus and T. persicus, were examined using partial nucleotide sequences of two mitochondrial genes (cytb and ND2) (total length 1,322 bp). Result Populations of T. sanguinolentus clustered within the T. agilis species complex, thus indicating its paraphyly, but T. sanguinolentus was previously determined to be a species based on morphological features. The T. agilis species complex forms two distinct major clades, each of which is represented by several local populations on the Iranian Plateau. At least five distinct taxa can be identified within this traditional group. Our biogeographic evaluation of the molecular dataset suggested that the Trapelus complex originated in the Late Oligocene (30 mya) and subsequently diversified during the early to middle Miocene (22–13 mya). At first, the predominantly western clade of Trapelus ruderatus diverged from the other clades (22 mya). Afterward, Trapelus persicus diverged around 18 mya ago. The broader T. agilis complex started to diverge about 16 mya, forming several clades on the Iranian Plateau and in Central Asia. The different lineages within this species complex appear to be the result of vicariance events and dispersal waives. The corresponding vicariance events are the formation of the Zagros and Kopet Dagh basins (16–14 mya), and consequently, the aridification of the Iranian Plateau in the late Miocene (11–6 Mya).
Shahamat et al. (2020) Molecular phylogeny and intraspecific differentiation of the Trapelus agilis species complex in Iran (Squamata: Agamidae) inferred from mitochondrial DNA sequences. PeerJ 8:e8295 https://doi.org/10.7717/peerj.8295
Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon
The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and stress responses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon–intron structure. Synteny analysis indicated the presence of a large number of syntenic relationship events between watermelon and cucumber. In promoter analysis, five kinds of stress-related and nine kinds of hormone-related cis-elements were identified in the promoter regions of ClDof genes. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of 12 selected ClDof genes under salt stress and ABA treatments using qRT-PCR. As a result, they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.
Zhou et al. (2020) Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon. PeerJ 8:e8358 https://doi.org/10.7717/peerj.8358